scholarly journals Identification of RING-H2 Gene Candidates Related to Wood Formation in Poplar

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 698
Author(s):  
Guimin Tong ◽  
Hongmei Shen ◽  
Shenquan Cao ◽  
Wenjing Xu ◽  
Xujun Ma ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Populus Trichocarpa ◽  
Microarray Dataset ◽  
Wood Formation ◽  
Multiple Gene ◽  
Poplar Genome ◽  
Gene Expression Analyses ◽  
Genes Encoding ◽  
Duplication Events ◽  
Ubiquitin Ligase E3

RING-H2 genes, the most abundant RING-type genes encoding putative ubiquitin ligase E3, are involved in diverse biological processes. Whether RING-H2 genes are related to wood formation remains to be identified in trees. In this study, we identified 288 RING-H2 genes in Populus trichocarpa, and found that the segmental and tandem duplication events contributed to RING-H2 gene expansion. Microarray dataset (from Affymetrix poplar genome arrays) showed that 64 of the 249 RING-H2 genes were highly or preferentially expressed in stem xylem. According to the AspWood RNAseq dataset, the transcription levels of genes PtrRHH21, 33, 48, 69, 88, 93, 94, 121, 141, 166, 175, 192, 208, 214, 250 and 257 were significantly increased in the xylem ranging from the expanding xylem to the lignifying xylem, suggesting their association with wood formation. Promoter analyses revealed that most of the preferentially xylem-expressed RING-H2 genes possessed SNBE, TERE, M46RE, AC and SMRE cis-elements, which are involved in secondary cell wall biosynthesis and programmed cell death. Based on the promoter GUS-based analysis result, PtrRHH94 was indicated to be associated with wood formation in transgenic P. trichocarpa. Taken together, dozens of Populus RING-H2 gene candidates associated with wood formation have been identified based on multiple gene expression analyses.

Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene familiesThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (12) ◽  
pp. 1182-1201 ◽  
Author(s):  
Björn Hamberger ◽  
Margaret Ellis ◽  
Michael Friedmann ◽  
Clarice de Azevedo Souza ◽  
Brad Barbazuk ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Populus Trichocarpa ◽  
Rice Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Comparative Approach ◽  
Expression Data ◽  
Poplar Genome ◽  
Genes Encoding ◽  
Bona Fide

The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar “lignification toolbox”) apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.

scholarly journals Functional Characterisation of the Poplar Atypical Aspartic Protease Gene PtAP66 in Wood Secondary Cell Wall Deposition

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1002
Author(s):  
Shenquan Cao ◽  
Cong Wang ◽  
Huanhuan Ji ◽  
Mengjie Guo ◽  
Jiyao Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Secondary Cell Wall ◽  
Fluorescent Protein ◽  
Secondary Xylem ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Protease Gene ◽  
Cellulose Content ◽  
Transcription Analysis ◽  
Functional Characterisation

Secondary cell wall (SCW) deposition is an important process during wood formation. Although aspartic proteases (APs) have been reported to have regulatory roles in herbaceous plants, the involvement of atypical APs in SCW deposition in trees has not been reported. In this study, we characterised the Populus trichocarpa atypical AP gene PtAP66, which is involved in wood SCW deposition. Transcriptome data from the AspWood resource showed that in the secondary xylem of P. trichocarpa, PtAP66 transcripts increased from the vascular cambium to the xylem cell expansion region and maintained high levels in the SCW formation region. Fluorescent signals from transgenic Arabidopsis plant roots and transiently transformed P. trichocarpa leaf protoplasts strongly suggested that the PtAP66-fused fluorescent protein (PtAP66-GFP or PtAP66-YFP) localised in the plasma membrane. Compared with the wild-type plants, the Cas9/gRNA-induced PtAP66 mutants exhibited reduced SCW thickness of secondary xylem fibres, as suggested by the scanning electron microscopy (SEM) data. In addition, wood composition assays revealed that the cellulose content in the mutants decreased by 4.90–5.57%. Transcription analysis further showed that a loss of PtAP66 downregulated the expression of several SCW synthesis-related genes, including cellulose and hemicellulose synthesis enzyme-encoding genes. Altogether, these findings indicate that atypical PtAP66 plays an important role in SCW deposition during wood formation.

scholarly journals Involvement of CesA4, CesA7-A/B and CesA8-A/B in secondary wall formation in Populus trichocarpa wood

2019 ◽  
Vol 40 (1) ◽  
pp. 73-89 ◽  
Author(s):  
Manzar Abbas ◽  
Ilona Peszlen ◽  
Rui Shi ◽  
Hoon Kim ◽  
Rui Katahira ◽  
...  
Keyword(s):  
Solid State ◽  
Mechanical Strength ◽  
Cell Walls ◽  
Secondary Wall ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Fiber Cell ◽  
Modulus Of Rupture ◽  
Cellulose Content ◽  
Wall Formation

Abstract Cellulose synthase A genes (CesAs) are responsible for cellulose biosynthesis in plant cell walls. In this study, functions of secondary wall cellulose synthases PtrCesA4, PtrCesA7-A/B and PtrCesA8-A/B were characterized during wood formation in Populus trichocarpa (Torr. & Gray). CesA RNAi knockdown transgenic plants exhibited stunted growth, narrow leaves, early necrosis, reduced stature, collapsed vessels, thinner fiber cell walls and extended fiber lumen diameters. In the RNAi knockdown transgenics, stems exhibited reduced mechanical strength, with reduced modulus of rupture (MOR) and modulus of elasticity (MOE). The reduced mechanical strength may be due to thinner fiber cell walls. Vessels in the xylem of the transgenics were collapsed, indicating that water transport in xylem may be affected and thus causing early necrosis in leaves. A dramatic decrease in cellulose content was observed in the RNAi knockdown transgenics. Compared with wildtype, the cellulose content was significantly decreased in the PtrCesA4, PtrCesA7 and PtrCesA8 RNAi knockdown transgenics. As a result, lignin and xylem contents were proportionally increased. The wood composition changes were confirmed by solid-state NMR, two-dimensional solution-state NMR and sum-frequency-generation vibration (SFG) analyses. Both solid-state nuclear magnetic resonance (NMR) and SFG analyses demonstrated that knockdown of PtrCesAs did not affect cellulose crystallinity index. Our results provided the evidence for the involvement of PtrCesA4, PtrCesA7-A/B and PtrCesA8-A/B in secondary cell wall formation in wood and demonstrated the pleiotropic effects of their perturbations on wood formation.

scholarly journals DIVARICATA AND RADIALIS INTERACTING FACTOR (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa

2018 ◽  
Vol 93 (6) ◽  
pp. 1076-1087 ◽  
Author(s):  
H. Earl Petzold ◽  
Bidisha Chanda ◽  
Chengsong Zhao ◽  
Stephen B. Rigoulot ◽  
Eric P. Beers ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Wood Formation ◽  
Knox Proteins

scholarly journals In silico identification of Capsicum type III polyketide synthase genes and expression patterns in Capsicum annuum

2020 ◽  
Vol 15 (1) ◽  
pp. 753-762
Author(s):  
Delong Kan ◽  
Di Zhao ◽  
Pengfei Duan
Keyword(s):  
Molecular Mechanisms ◽  
Polyketide Synthase ◽  
Expression Patterns ◽  
Class Ii ◽  
Chili Pepper ◽  
Type Iii Polyketide Synthase ◽  
Type Iii ◽  
Genes Encoding ◽  
Duplication Events ◽  
Pepper Leaves

AbstractStudies have shown that abundant and various flavonoids accumulate in chili pepper (Capsicum), but there are few reports on the genes that govern chili pepper flavonoid biosynthesis. Here, we report the comprehensive identification of genes encoding type III polyketide synthase (PKS), an important enzyme catalyzing the generation of flavonoid backbones. In total, 13, 14 and 13 type III PKS genes were identified in each genome of C. annuum, C. chinense and C. baccatum, respectively. The phylogeny topology of Capsicum PKSs is similar to those in other plants, as it showed two classes of genes. Within each class, clades can be further identified. Class II genes likely encode chalcone synthase (CHS) as they are placed together with the Arabidopsis CHS gene, which experienced extensive expansions in the genomes of Capsicum. Interestingly, 8 of the 11 Class II genes form three clusters in the genome of C. annuum, which is likely the result of tandem duplication events. Four genes are not expressed in the tissues of C. annuum, three of which are located in the clusters, indicating that a portion of genes was pseudogenized after tandem duplications. Expression of two Class I genes was complementary to each other, and all the genes in Class II were not expressed in roots of C. annuum. Two Class II genes (CA00g90790 and CA05g17060) showed upregulated expression as the chili pepper leaves matured, and two Class II genes (CA05g17060 and CA12g20070) showed downregulated expression with the maturation of fruits, consistent with flavonoid accumulation trends in chili pepper as reported previously. The identified genes, sequences, phylogeny and expression information collected in this article lay the groundwork for future studies on the molecular mechanisms of chili pepper flavonoid metabolism.

scholarly journals Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262370
Author(s):  
Jordan C. Raisman ◽  
Michael A. Fiore ◽  
Lucille Tomin ◽  
Joseph K. O. Adjei ◽  
Virginia X. Aswad ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Natural Populations ◽  
Growth Defect ◽  
Duplication Events ◽  
Pathogen Populations ◽  
High Level ◽  
Evolutionary Paths ◽  
Azithromycin Resistance ◽  
Short Tandem

Neisseria commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≥ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n = 7/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in rpmH is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.

scholarly journals Diversification of Genes Encoding Granule-Bound Starch Synthase in Monocots and Dicots Is Marked by Multiple Genome-Wide Duplication Events

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e30088 ◽  
Author(s):  
Jun Cheng ◽  
Muhammad Awais Khan ◽  
Wen-Ming Qiu ◽  
Jing Li ◽  
Hui Zhou ◽  
...  
Keyword(s):  
Starch Synthase ◽  
Multiple Genome ◽  
Genome Wide ◽  
Genes Encoding ◽  
Duplication Events ◽  
Granule Bound Starch Synthase

Clone and Analysis of Secondary Xylem Cellulose Synthase Gene Fragment from Populus ussuriensis

2010 ◽  
Vol 113-116 ◽  
pp. 1908-1913
Author(s):  
Jiang Tao Shi ◽  
Jian Li ◽  
Yi Xing Liu ◽  
Lei Xu
Keyword(s):  
Populus Tremuloides ◽  
Gene Sequence ◽  
Secondary Xylem ◽  
Sequence Similarity ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Cellulose Synthase ◽  
Cellulose Synthase Gene ◽  
Populus Ussuriensis ◽  
Close Genetic Relationship

wood is the most abundant renewable resource and environmentally friendly energy source on the earth, it not only provides industrial raw materials for economic and social sustainable development, meanwhile, the biological process of wood formation which is mainly to sink the excessive carbon dioxide in the atmosphere can also play an active role in reducing “greenhouse effect”, so it is the contributor of green environment and human heath. Therefore, it is of great importance to explore the biosynthesis process and the wood formation mechanism of woods cellulose. This study adopted RT-PCR to clone gene fragments from the total RNA of populus ussuriensis secondary xylem, through sequence analysis, we found that its size was 487bp, which was named as PusC1，by means of blast comparative analysis, we found that the gene sequence similarity of this fragment and Populus trichocarpa cellulose synthase (XM 002305024.1) reached 94%, and its gene sequence similarity with Populus tremuloides PtrCesA1 and Populus tremula × Populus tremuloides xylem specificity cellulose synthase genes (AY573574.1) sequence could also reach 92%. Therefore, it is inferred to be populus ussuriensis xylem specificity cellulose synthase gene fragment. Through sequence similarity, we can also infer that populus ussuriensis has a close genetic relationship with Populus trichocarpa and belongs to cathay poplar species; while Populus tremuloides belongs to white poplar species and has a close genetic relationship with populus ussuriensis.

scholarly journals Phylogenetic, Expression, and Bioinformatic Analysis of theABC1Gene Family inPopulus trichocarpa

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Zhanchao Wang ◽  
Haizhen Zhang ◽  
Jingli Yang ◽  
Yunlin Chen ◽  
Xuemei Xu ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Signal Transduction Pathway ◽  
Bioinformatic Analysis ◽  
Wood Formation ◽  
Cellulose Synthesis ◽  
Amino Acid Residues ◽  
Element Analysis ◽  
Aba Signal Transduction ◽  
Almost All

We studied 17ABC1genes inPopulus trichocarpa, all of which contained anABC1domain consisting of about 120 amino acid residues. Most of theABC1gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19Populuschromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap,PtrABC1P14was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promotercis-element analysis indicated that almost all of theABC1genes contained one or twocis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promotercis-element analysis.

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